inmembrane_scan

#!/usr/bin/env python
# Copyright (c) 2012, Bosco Ho <boscoh@gmail.com>
# Copyright (c) 2012, Andrew Perry <ajperry@pansapiens.com>
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or
# without modification, are permitted provided that the following 
# conditions are met:

# 1. Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# 2. Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the 
# documentation and/or other materials provided with the distribution.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS 
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT 
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS 
# FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE 
# COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, 
# INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, 
# BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS 
# OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED 
# AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF 
# THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH 
# DAMAGE.

import sys
import os
import glob

import inmembrane
# from inmembrane import helpers
from inmembrane.helpers import *
# will load all plugins in the plugins/ directory
from inmembrane.plugins import *
import unittest

description = """
inmembrane %s (https://github.com/boscoh/inmembrane)

Inmembrane is a proteome annotation pipeline. It takes 
a FASTA file, then carries out sequential analysis of 
each sequence with a bunch of third-party programs, and 
collates the results.

(c) 2011-2013 Bosco Ho and Andrew Perry
""" % (inmembrane.__version__)

if __name__ == "__main__":
    from optparse import OptionParser

    usage = "usage: %prog [options] [sequences.fasta]"
    parser = OptionParser(usage=usage, \
                          version="%prog " + inmembrane.__version__ + "\n", )
    parser.add_option("-t", "--test",
                      action="store_true", dest="run_tests", default=False,
                      help="Run tests to check that each plugin works as expected.\
                          No sequence file should be specified if this flag is\
                          used.")
    parser.add_option("-n", "--tests-no-network",
                      action="store_true", dest="no_network", default=False,
                      help="don't run tests that require a network connection")
    parser.add_option("--skip-tests",
                      action="store", type="string", dest="skip_tests",
                      help="a comma separated list of tests to skip eg: "
                           "test_tmhmm_web,test_lipop_web")
    (options, args) = parser.parse_args()

    log_stderr("inmembrane %s (https://github.com/boscoh/inmembrane)"
               % (inmembrane.__version__))

    if not options.run_tests:
        ##
        ## Setup params and run the analysis
        ## The high level plugin loop is in inmembrane/__init__.py
        ##

        params = inmembrane.get_params()
        if ('fasta' not in params or not params['fasta']) and not args:
            print description
            parser.print_help()
            sys.exit(1)
        if 'fasta' not in params or not params['fasta']:
            params['fasta'] = args[0]
        inmembrane.process(params)

    else:
        ##
        ## Run unit tests instead of 'normal' analysis
        ##

        log_stderr("Running tests")

        skip_list = []
        if "--skip-tests" in sys.argv:
            skip_list = [tn.strip() for tn in options.skip_tests.split(',')]
            log_stderr("Will skip: " + ", ".join(skip_list))
            # sys.argv.remove("--skip-tests")

        file_tag = os.path.join(inmembrane.module_dir, 'tests', 'test*.py')
        test_names = [os.path.basename(f)[:-3] for f in glob.glob(file_tag)]

        tests_to_run = []
        for test_name in test_names:
            if not (options.no_network and (test_name[-4:] == "_web")):
                if (test_name not in skip_list):
                    exec ('from inmembrane.tests.%s import *' % test_name)
                    tests_to_run.append(test_name)

        log_stderr("Will run: " + ", ".join(tests_to_run))

        log_stderr("\n")
        log_stderr(
            "Note that it isn't unusual for some tests to "
            "fail - only be concerned with the particular analysis "
            "tools you will run, as defined in inmembrane.config. "
            "Errors can occur due to a missing locally installed "
            "program or a web service being temporarily or permanently "
            "offline.\n")
        log_stderr("\n")
        if ("test_memsat3" in test_names):
            log_stderr(
                "Note that MEMSAT3 tests will likely fail even when "
                "MEMSAT3 is functioning correctly since the results are "
                "dependant on a BLAST search and the locally installed "
                "BLAST database is unlikely to match the one used to "
                "derive the test results. If the numbers are similar it "
                "should be okay.\n")
            log_stderr("\n")

        # by passing in argv we override unittests own commandline option
        # detection
        unittest.main(argv=[os.path.basename(sys.argv[0])])